molstar 3.0.0-dev.8 → 3.0.2

package/lib/mol-gl/renderer.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -37,7 +37,7 @@ export declare const enum MarkingType {
 interface Renderer {
     readonly stats: RendererStats;
     readonly props: Readonly<RendererProps>;
-    clear: (toBackgroundColor: boolean) => void;
+    clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => void;
     clearDepth: () => void;
     update: (camera: ICamera) => void;
     renderPick: (group: Scene.Group, camera: ICamera, variant: GraphicsRenderVariant, depthTexture: Texture | null, pickType: PickType) => void;

package/lib/mol-gl/renderer.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -379,12 +379,12 @@ var Renderer;
             }
         };
         return {
-            clear: function (toBackgroundColor) {
+            clear: function (toBackgroundColor, ignoreTransparentBackground) {
                 state.enable(gl.SCISSOR_TEST);
                 state.enable(gl.DEPTH_TEST);
                 state.colorMask(true, true, true, true);
                 state.depthMask(true);
-                if (transparentBackground) {
+                if (transparentBackground && !ignoreTransparentBackground) {
                     state.clearColor(0, 0, 0, 0);
                 }
                 else if (toBackgroundColor) {

package/lib/mol-io/reader/cif/schema/bird.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/bird.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/ccd.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/ccd.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/mmcif.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.353, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */
@@ -670,7 +670,7 @@ export declare const mmCIF_Schema: {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Schema.Aliased<"CAS" | "CSD" | "EMDB" | "ICSD" | "MDF" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
+        database_id: Schema.Aliased<"AFDB" | "CAS" | "CSD" | "EMDB" | "ICSD" | "MA" | "MDF" | "MODBASE" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "SMR" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.

package/lib/mol-io/reader/cif/schema/mmcif.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.353, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/mol/parser.d.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { Column } from '../../../mol-data/db';
 import { Task } from '../../../mol-task';
@@ -18,6 +19,7 @@ export interface MolFile {
         readonly y: Column<number>;
         readonly z: Column<number>;
         readonly type_symbol: Column<string>;
+        readonly formal_charge: Column<number>;
     };
     readonly bonds: {
         readonly count: number;
@@ -25,7 +27,27 @@ export interface MolFile {
         readonly atomIdxB: Column<number>;
         readonly order: Column<number>;
     };
+    readonly formalCharges: {
+        readonly atomIdx: Column<number>;
+        readonly charge: Column<number>;
+    };
 }
+/**
+ * @param key - The value found at the atom block.
+ * @returns The actual formal charge based on the mapping.
+ */
+export declare function formalChargeMapper(key: number): 0 | 1 | 3 | 2 | -3 | -1 | -2;
 export declare function handleAtoms(tokenizer: Tokenizer, count: number): MolFile['atoms'];
 export declare function handleBonds(tokenizer: Tokenizer, count: number): MolFile['bonds'];
+interface FormalChargesRawData {
+    atomIdx: Array<number>;
+    charge: Array<number>;
+}
+export declare function handleFormalCharges(tokenizer: Tokenizer, lineStart: number, formalCharges: FormalChargesRawData): void;
+/** Call an appropriate handler based on the property type.
+ * (For now it only calls the formal charge handler, additional handlers can
+ * be added for other properties.)
+ */
+export declare function handlePropertiesBlock(tokenizer: Tokenizer): MolFile['formalCharges'];
 export declare function parseMol(data: string): Task<Result<MolFile>>;
+export {};

package/lib/mol-io/reader/mol/parser.js

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { __awaiter, __generator } from "tslib";
 import { Column } from '../../../mol-data/db';
@@ -9,11 +10,57 @@ import { Task } from '../../../mol-task';
 import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
 import { TokenBuilder, Tokenizer } from '../common/text/tokenizer';
 import { ReaderResult as Result } from '../result';
+/*
+    The atom lines in a .mol file have the following structure:
+
+    xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
+    ---------------------------------------------------------------------
+
+    Below is a breakdown of each component and its start/end indices:
+
+    xxxxx.xxxx  (X COORDINATE, 1-10)
+    yyyyy.yyyy  (Y COORDINATE, 10-20)
+    zzzzz.zzzz  (Z COORDINATE, 20-30)
+    _           (30 IS EMPTY)
+    aaa         (ATOM SYMBOL, 31-34)
+    dd          (MASS DIFF, 34-36)
+    ccc         (FORMAL CHARGE, 36-39)
+    sss         (ATOM STEREO PARITY, 39-42)
+    hhh         (HYDROGEN COUNT+1, 42-45)
+    bbb         (STEREO CARE BOX, 45-48)
+    vvv         (VALENCE, 48-51)
+    HHH         (H0 DESIGNATOR, 51-54)
+    rrr         (UNUSED, 54-57)
+    iii         (UNUSED, 57-60)
+    mmm         (ATOM-ATOM MAPPING NUMBER, 60-63)
+    nnn         (INVERSION/RETENTION FLAG, 63-66)
+    eee         (EXACT CHANGE FLAG, 66-69)
+*/
+/**
+ * @param key - The value found at the atom block.
+ * @returns The actual formal charge based on the mapping.
+ */
+export function formalChargeMapper(key) {
+    switch (key) {
+        case 7: return -3;
+        case 6: return -2;
+        case 5: return -1;
+        case 0: return 0;
+        case 3: return 1;
+        case 2: return 2;
+        case 1: return 3;
+        case 4: return 0;
+        default:
+            console.error("Value ".concat(key, " is outside the 0-7 range, defaulting to 0."));
+            return 0;
+    }
+}
 export function handleAtoms(tokenizer, count) {
     var x = TokenBuilder.create(tokenizer.data, count * 2);
     var y = TokenBuilder.create(tokenizer.data, count * 2);
     var z = TokenBuilder.create(tokenizer.data, count * 2);
     var type_symbol = TokenBuilder.create(tokenizer.data, count * 2);
+    var formal_charge = TokenBuilder.create(tokenizer.data, count * 2);
     for (var i = 0; i < count; ++i) {
         Tokenizer.markLine(tokenizer);
         var s = tokenizer.tokenStart, position = tokenizer.position;
@@ -25,6 +72,8 @@ export function handleAtoms(tokenizer, count) {
         TokenBuilder.addUnchecked(z, tokenizer.tokenStart, tokenizer.tokenEnd);
         Tokenizer.trim(tokenizer, s + 31, s + 34);
         TokenBuilder.addUnchecked(type_symbol, tokenizer.tokenStart, tokenizer.tokenEnd);
+        Tokenizer.trim(tokenizer, s + 36, s + 39);
+        TokenBuilder.addUnchecked(formal_charge, tokenizer.tokenStart, tokenizer.tokenEnd);
         tokenizer.position = position;
     }
     return {
@@ -32,7 +81,8 @@ export function handleAtoms(tokenizer, count) {
         x: TokenColumn(x)(Column.Schema.float),
         y: TokenColumn(y)(Column.Schema.float),
         z: TokenColumn(z)(Column.Schema.float),
-        type_symbol: TokenColumn(type_symbol)(Column.Schema.str)
+        type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+        formal_charge: TokenColumn(formal_charge)(Column.Schema.int)
     };
 }
 export function handleBonds(tokenizer, count) {
@@ -57,6 +107,63 @@ export function handleBonds(tokenizer, count) {
         order: TokenColumn(order)(Column.Schema.int)
     };
 }
+export function handleFormalCharges(tokenizer, lineStart, formalCharges) {
+    Tokenizer.trim(tokenizer, lineStart + 6, lineStart + 9);
+    var numOfCharges = parseInt(Tokenizer.getTokenString(tokenizer));
+    for (var i = 0; i < numOfCharges; ++i) {
+        /*
+        M  CHG  3   1  -1   2   0   2  -1
+                |   |   |   |   |
+                |   |   |   |   |__charge2 (etc.)
+                |   |   |   |
+                |   |   |   |__atomIdx2
+                |   |   |
+                |   |   |__charge1
+                |   |
+                |   |__atomIdx1 (cursor at position 12)
+                |
+                |___numOfCharges
+        */
+        var offset = 9 + (i * 8);
+        Tokenizer.trim(tokenizer, lineStart + offset, lineStart + offset + 4);
+        var _atomIdx = Tokenizer.getTokenString(tokenizer);
+        formalCharges.atomIdx.push(+_atomIdx);
+        Tokenizer.trim(tokenizer, lineStart + offset + 4, lineStart + offset + 8);
+        var _charge = Tokenizer.getTokenString(tokenizer);
+        formalCharges.charge.push(+_charge);
+    }
+    /* Once the line is read, move to the next one. */
+    Tokenizer.eatLine(tokenizer);
+}
+/** Call an appropriate handler based on the property type.
+ * (For now it only calls the formal charge handler, additional handlers can
+ * be added for other properties.)
+ */
+export function handlePropertiesBlock(tokenizer) {
+    var _atomIdx = [];
+    var _charge = [];
+    var _formalCharges = { atomIdx: _atomIdx, charge: _charge };
+    while (tokenizer.position < tokenizer.length) {
+        var s = tokenizer.position;
+        Tokenizer.trim(tokenizer, s + 3, s + 6);
+        var propertyType = Tokenizer.getTokenString(tokenizer);
+        if (propertyType === 'END')
+            break;
+        Tokenizer.eatLine(tokenizer);
+        switch (propertyType) {
+            case 'CHG':
+                handleFormalCharges(tokenizer, s, _formalCharges);
+                break;
+            default:
+                break;
+        }
+    }
+    var formalCharges = {
+        atomIdx: Column.ofIntArray(_formalCharges.atomIdx),
+        charge: Column.ofIntArray(_formalCharges.charge)
+    };
+    return formalCharges;
+}
 function parseInternal(data) {
     var tokenizer = Tokenizer(data);
     var title = Tokenizer.readLine(tokenizer).trim();
@@ -66,12 +173,14 @@ function parseInternal(data) {
     var atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
     var atoms = handleAtoms(tokenizer, atomCount);
     var bonds = handleBonds(tokenizer, bondCount);
+    var formalCharges = handlePropertiesBlock(tokenizer);
     var result = {
         title: title,
         program: program,
         comment: comment,
         atoms: atoms,
-        bonds: bonds
+        bonds: bonds,
+        formalCharges: formalCharges,
     };
     return Result.success(result);
 }

package/lib/mol-io/reader/mol2/parser.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-io/reader/mol2/parser.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -241,9 +241,38 @@ function handleBonds(state) {
         });
     });
 }
+function handleCrysin(state) {
+    var tokenizer = state.tokenizer;
+    while (tokenizer.position < tokenizer.data.length) {
+        var l = getTokenString(tokenizer);
+        if (l === '@<TRIPOS>MOLECULE') {
+            return;
+        }
+        else if (l === '@<TRIPOS>CRYSIN') {
+            break;
+        }
+        else {
+            markLine(tokenizer);
+        }
+    }
+    if (tokenizer.position >= tokenizer.data.length)
+        return;
+    markLine(tokenizer);
+    var values = getTokenString(tokenizer).trim().split(reWhitespace);
+    return {
+        a: parseFloat(values[0]),
+        b: parseFloat(values[1]),
+        c: parseFloat(values[2]),
+        alpha: parseFloat(values[3]),
+        beta: parseFloat(values[4]),
+        gamma: parseFloat(values[5]),
+        spaceGroup: parseInt(values[6], 10),
+        setting: parseInt(values[7], 10),
+    };
+}
 function parseInternal(ctx, data, name) {
     return __awaiter(this, void 0, void 0, function () {
-        var tokenizer, structures, state, atoms, bonds, result;
+        var tokenizer, structures, state, atoms, bonds, crysin, result;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -261,7 +290,8 @@ function parseInternal(ctx, data, name) {
                     return [4 /*yield*/, handleBonds(state)];
                 case 3:
                     bonds = _a.sent();
-                    structures.push({ molecule: state.molecule, atoms: atoms, bonds: bonds });
+                    crysin = handleCrysin(state);
+                    structures.push({ molecule: state.molecule, atoms: atoms, bonds: bonds, crysin: crysin });
                     skipWhitespace(tokenizer);
                     while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE' && tokenizer.position < tokenizer.data.length) {
                         markLine(tokenizer);

package/lib/mol-io/reader/mol2/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -37,10 +37,21 @@ export interface Mol2Bonds {
     bond_type: Column<string>;
     status_bits: Column<string>;
 }
+export interface Mol2Crysin {
+    a: number;
+    b: number;
+    c: number;
+    alpha: number;
+    beta: number;
+    gamma: number;
+    spaceGroup: number;
+    setting: number;
+}
 export interface Mol2Structure {
     molecule: Readonly<Mol2Molecule>;
     atoms: Readonly<Mol2Atoms>;
     bonds: Readonly<Mol2Bonds>;
+    crysin?: Readonly<Mol2Crysin>;
 }
 export interface Mol2File {
     name: string;

package/lib/mol-io/reader/mol2/schema.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-io/reader/sdf/parser-v3-util.d.ts

@@ -1,3 +1,9 @@
+/**
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
 import { MolFile } from '../mol/parser';
 import { Tokenizer } from '../common/text/tokenizer';
 export declare function isV3(versionLine: string): boolean;

package/lib/mol-io/reader/sdf/parser-v3-util.js

@@ -1,3 +1,9 @@
+/**
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
 import { Column } from '../../../mol-data/db';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
 import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
@@ -44,6 +50,9 @@ export function handleAtomsV3(tokenizer, atomCount) {
         y: TokenColumn(y)(Column.Schema.float),
         z: TokenColumn(z)(Column.Schema.float),
         type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+        /* No support for formal charge parsing in V3000 molfiles at the moment,
+        so all charges default to 0.*/
+        formal_charge: Column.ofConst(0, atomCount, Column.Schema.int)
     };
 }
 export function handleBondsV3(tokenizer, bondCount) {

package/lib/mol-io/reader/sdf/parser.d.ts

@@ -1,8 +1,10 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { Column } from '../../../mol-data/db';
 import { MolFile } from '../mol/parser';

package/lib/mol-io/reader/sdf/parser.js

@@ -1,12 +1,14 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { __awaiter, __generator } from "tslib";
 import { Column } from '../../../mol-data/db';
-import { handleAtoms, handleBonds } from '../mol/parser';
+import { handleAtoms, handleBonds, handlePropertiesBlock } from '../mol/parser';
 import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
@@ -69,11 +71,18 @@ function handleMolFile(tokenizer) {
         }
         return;
     }
+    /* No support for formal charge parsing in V3000 molfiles at the moment,
+    so all charges default to 0.*/
+    var nullFormalCharges = {
+        atomIdx: Column.ofConst(0, atomCount, Column.Schema.int),
+        charge: Column.ofConst(0, atomCount, Column.Schema.int)
+    };
     var atoms = molIsV3 ? handleAtomsV3(tokenizer, atomCount) : handleAtoms(tokenizer, atomCount);
     var bonds = molIsV3 ? handleBondsV3(tokenizer, bondCount) : handleBonds(tokenizer, bondCount);
+    var formalCharges = molIsV3 ? nullFormalCharges : handlePropertiesBlock(tokenizer);
     var dataItems = handleDataItems(tokenizer);
     return {
-        molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds },
+        molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds, formalCharges: formalCharges },
         dataItems: dataItems
     };
 }

package/lib/mol-io/writer/cif/encoder/binary.js

@@ -170,8 +170,15 @@ function getFieldData(field, arrayCtor, totalCount, data) {
                 allPresent = false;
             }
             else {
-                mask[offset] = 0 /* Present */;
-                array[offset] = getter(key, d, offset);
+                var value = getter(key, d, offset);
+                if (typeof value === 'string' && !value) {
+                    mask[offset] = 1 /* NotPresent */;
+                    allPresent = false;
+                }
+                else {
+                    mask[offset] = 0 /* Present */;
+                }
+                array[offset] = value;
             }
             offset++;
         }

package/lib/mol-math/geometry/primitives/sphere3d.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-math/geometry/primitives/sphere3d.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -7,6 +7,8 @@
 import { __spreadArray } from "tslib";
 import { Vec3, Mat4, EPSILON } from '../../linear-algebra';
 import { OrderedSet } from '../../../mol-data/int';
+import { Axes3D } from './axes3d';
+import { PrincipalAxes } from '../../linear-algebra/matrix/principal-axes';
 function Sphere3D() {
     return Sphere3D.zero();
 }
@@ -193,11 +195,22 @@ function Sphere3D() {
             return out;
         }
         if (hasExtrema(sphere)) {
+            var positions = new Float32Array(sphere.extrema.length * 3);
+            for (var i = 0; i < sphere.extrema.length; i++) {
+                Vec3.toArray(sphere.extrema[i], positions, i * 3);
+            }
+            var axes_1 = PrincipalAxes.calculateMomentsAxes(positions);
+            Axes3D.scale(axes_1, Axes3D.normalize(axes_1, axes_1), delta);
             setExtrema(out, sphere.extrema.map(function (e) {
                 Vec3.sub(tmpDir, e, sphere.center);
-                var dist = Vec3.distance(sphere.center, e);
-                Vec3.normalize(tmpDir, tmpDir);
-                return Vec3.scaleAndAdd(Vec3(), sphere.center, tmpDir, dist + delta);
+                var out = Vec3.clone(e);
+                var sA = Vec3.dot(tmpDir, axes_1.dirA) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes_1.dirA, sA);
+                var sB = Vec3.dot(tmpDir, axes_1.dirB) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes_1.dirB, sB);
+                var sC = Vec3.dot(tmpDir, axes_1.dirC) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes_1.dirC, sC);
+                return out;
             }));
         }
         return out;

package/lib/mol-math/geometry/symmetry-operator.d.ts

@@ -42,7 +42,7 @@ declare namespace SymmetryOperator {
         hkl?: Vec3;
         spgrOp?: number;
     };
-    function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator;
+    function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator;
     function checkIfRotationAndTranslation(rot: Mat3, offset: Vec3): boolean;
     function ofRotationAndOffset(name: string, rot: Mat3, offset: Vec3, ncsId?: number): SymmetryOperator;
     function lerpFromIdentity(out: Mat4, op: SymmetryOperator, t: number): Mat4;

package/lib/mol-math/geometry/symmetry-operator.js

@@ -19,8 +19,9 @@ var SymmetryOperator;
         var _hkl = hkl ? Vec3.clone(hkl) : Vec3();
         spgrOp = defaults(spgrOp, -1);
         ncsId = ncsId || -1;
-        var suffix = getSuffix(info);
-        if (Mat4.isIdentity(matrix))
+        var isIdentity = Mat4.isIdentity(matrix);
+        var suffix = getSuffix(info, isIdentity);
+        if (isIdentity)
             return { name: name, assembly: assembly, matrix: matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
         if (!Mat4.isRotationAndTranslation(matrix, SymmetryOperator.RotationTranslationEpsilon)) {
             console.warn("Symmetry operator (".concat(name, ") should be a composition of rotation and translation."));
@@ -28,11 +29,16 @@ var SymmetryOperator;
         return { name: name, assembly: assembly, matrix: matrix, inverse: Mat4.invert(Mat4(), matrix), isIdentity: false, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
     }
     SymmetryOperator.create = create;
-    function getSuffix(info) {
+    function isSymmetryOperator(x) {
+        return !!x && !!x.matrix && !!x.inverse && typeof x.name === 'string';
+    }
+    function getSuffix(info, isIdentity) {
         if (!info)
             return '';
         if (info.assembly) {
-            return "_".concat(info.assembly.operId);
+            if (isSymmetryOperator(info))
+                return info.suffix;
+            return isIdentity ? '' : "_".concat(info.assembly.operId);
         }
         if (typeof info.spgrOp !== 'undefined' && typeof info.hkl !== 'undefined' && info.spgrOp !== -1) {
             var _a = info.hkl, i = _a[0], j = _a[1], k = _a[2];

package/lib/mol-model/structure/export/mmcif.d.ts

@@ -28,5 +28,5 @@ declare type encode_mmCIF_categories_Params = {
 };
 /** Doesn't start a data block */
 export declare function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures: Structure | Structure[], params?: encode_mmCIF_categories_Params): void;
-declare function to_mmCIF(name: string, structure: Structure, asBinary?: boolean): string | Uint8Array;
+declare function to_mmCIF(name: string, structure: Structure, asBinary?: boolean, params?: encode_mmCIF_categories_Params): string | Uint8Array;
 export { to_mmCIF };